I know that in real life, Bill Cosby and Lisa Bonet had another falling out. So asking her to come back for the series finale would've been out of the question considering the circumstances.

And they did try to explain Denise's absence her call from wherever Martin was supposed to have been stationed to say she was pregnant.

But even so, does it still feel awfully weird that Denise in the context of the show, couldn't make it to a momentous event like her brother's graduation?

Yes, Denise "phoning it in" (off camera) was weird. I guess it's better that they acknowledged her character than to just not mention her, like Chuck Cunningham, but more ideal would have been to have invited Lisa Bonet back. I've heard she was not asked back, which would have been Bill Cosby's decision.